Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

Handle URI:
http://hdl.handle.net/10754/325281
Title:
Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
Authors:
Wang, Yong; Qian, Pei-Yuan
Abstract:
Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.
Citation:
Wang Y, Qian P-Y (2009) Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies. PLoS ONE 4: e7401. doi:10.1371/journal.pone.0007401.
Publisher:
Public Library of Science
Journal:
PLoS ONE
Issue Date:
9-Oct-2009
DOI:
10.1371/journal.pone.0007401
PubMed ID:
19816594
PubMed Central ID:
PMC2754607
Type:
Article
ISSN:
19326203
Sponsors:
KAUST Global Partnership. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Yongen
dc.contributor.authorQian, Pei-Yuanen
dc.date.accessioned2014-08-27T09:44:43Z-
dc.date.available2014-08-27T09:44:43Z-
dc.date.issued2009-10-09en
dc.identifier.citationWang Y, Qian P-Y (2009) Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies. PLoS ONE 4: e7401. doi:10.1371/journal.pone.0007401.en
dc.identifier.issn19326203en
dc.identifier.pmid19816594en
dc.identifier.doi10.1371/journal.pone.0007401en
dc.identifier.urihttp://hdl.handle.net/10754/325281en
dc.description.abstractBacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.en
dc.description.sponsorshipKAUST Global Partnership. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rightsWang, Qian. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjectbacterial DNAen
dc.subjectbacterial RNAen
dc.subjectDNA 16Sen
dc.subjectRNA 16Sen
dc.subjectprimer DNAen
dc.subjectribosome DNAen
dc.subjectbacterial geneen
dc.subjectcontrolled studyen
dc.subjectgene amplificationen
dc.subjectgenetic conservationen
dc.subjectgenomic fragmenten
dc.subjectmetagenomicsen
dc.subjectphylumen
dc.subjectRNA sequenceen
dc.subjectarchaebacteriumen
dc.subjectbacteriumen
dc.subjectcyanobacteriumen
dc.subjectEscherichia colien
dc.subjectgenetic databaseen
dc.subjectgenetic polymorphismen
dc.subjectgeneticsen
dc.subjectgenomicsen
dc.subjectmethodologyen
dc.subjectBacteria (microorganisms)en
dc.subjectFirmicutesen
dc.subjectGemmatimonadetesen
dc.subjectProteobacteriaen
dc.subjectuncultured bacteriumen
dc.subjectArchaeaen
dc.subjectBacteriaen
dc.subjectCyanobacteriaen
dc.subjectDatabases, Geneticen
dc.subjectDNA Primersen
dc.subjectDNA, Ribosomalen
dc.subjectEscherichia colien
dc.subjectGenes, Bacterialen
dc.subjectGenomicsen
dc.subjectMetagenomicsen
dc.subjectPolymorphism, Geneticen
dc.subjectRNA, Bacterialen
dc.subjectRNA, Ribosomal, 16Sen
dc.titleConservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studiesen
dc.typeArticleen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC2754607en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionUnidad Académica de Sistemas Arrecifales (Puerto Morelos), Instituto de Ciencias Del Mar y Limnología, Universidad Nacional Autõnoma de México, Puerto Morelos, QR 77580, Mexicoen
dc.contributor.institutionSchool of Natural Sciences, University of California Merced, 5200 North Lake Road, Merced, CA 95343, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.grant.programKAUST Global Partnership Programen

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